It must be a loose wire going to the roller pots, coz if the neck pickup works on the lead circuit then its obviously not the pickup. A previous owner may have disconnected it with the idea of making the top switch a 'killswitch', its not a popular circuit.
The best thing to do is compare your wiring to a diagram.
If you look at this diagram the two wires at the bottom of the switch go to the tone and volume, make sure they are connected. Also check the orange wire from the lower switch is connected up to the top switch.
http://www.guitarnucleus.com/gitschems/Jaguar62_wir.jpg
